Hi Freddie,
I would like to answer these questions one by one.
Q1: What is the difference between a user I create manually and a user that was initially created with DirSync?
A1: In this case, if the user is synchronized from on-premise AD, many Exchange-related are synchronized during the user is created at Office 365 side.
If the user is created at Office 365 side directly, these attributes are not set during the user creation.
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Q2: There must be a parameter that defines this that I can change??
A2: Currently, there is no way to prevent these attributes from being synchronized when synchronizing the user or remove these attributes after synchronization.
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Q3: Alternatively, perhaps there is a organisational parameter that defines that the organisation is still in hybrid mode that can be changed?
A3: Currently, a specific parameter to define whether the Office 365 tenant is in Hybrid mode is not available.
In this case, many Exchange-related attributes are synchronized indicate that the user has mailboxes at other Exchange servers. Moreover, some of these attributes cannot be modified or removed at cloud side directly, such as LegacyExchangeDN.
As a result, given this situation, these users need to be deleted at cloud side and to be re-created manually. As a tip, you may also refer to the following article to add multiple users with bulk import:
http://onlinehelp.microsoft.com/en-us/office365-enterprises/ff637601.aspx
Thanks,
Claud